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Table 1 Putative alternate splice variants of MYB and RT-PCR results testing their existence.

From: Genome annotation of a 1.5 Mb region of human chromosome 6q23 encompassing a quantitative trait locus for fetal hemoglobin expression in adults

 

Evidence

   

Putative Alternate exon

Literature

Existing sequence

EST Evidence

Ensembl transcript

Gene Prediction

Conserved region with mouse

RT-PCR primer sequences:

Positive result by RT-PCR (PCR conditions)

Sequence Accession Number

1A

    

 

F: GCCCGAAGACCCCGGCACAG

R:TGCAACTTCCCAGCGCCGCG

  

1B

     

F: GCCCGAAGACCCCGGCACAG

R:CCAACAGTCAGAGGATTTTCAAAG

  

1C

     

F: GCCCGAAGACCCCGGCACAG

R:CAATGCATCCAGCAATTACG

  

1D

     

F: GCCCGAAGACCCCGGCACAG

R:GGCCACTTGTTAGTCAGAGTCTT

  

1E

    

 

F: GCCCGAAGACCCCGGCACAG

R:TACACATTTGGCCACCTTCC

  

2'

[22]

X52125

    

F: GCCCGAAGACCCCGGCACAG

R:TGCAGAAATAAGAATGGGTAGACG

  

5A

    

 

F: GCCCTGCTGTGCCACATTCAAA

R:CGGAGCCTGAGCAAAACCCATC

  

8'

[22]

X52125

   

F: AAATATAGTCAATGTCCCTCAGCC

R:ATGTGTGGTTCTGTGTCTGCTGT

2.5 mM/60C

AJ606320

8-extended

[23]

M13666

   

F: AAATATAGTCAATGTCCCTCAGCC

R:ACAAAATAATAGAAAAAAACCAAAATG

  

8A

[22]

U22376, X52125

 

  

F: AAATATAGTCAATGTCCCTCAGCC

R:GGGCATCACTTCTCTTTTATTGTCT

1.5 mM, 60C

AJ606317

8A-extended

  

  

F: AAATATAGTCAATGTCCCTCAGCC

R:GCACATGCTAGTTCGACCAC

  

9Ai

 

U22376

    

F: ACAGAACCACACATGCAGCTACC

R:TGAAACAGCACTGAGAGAGAGATG

2.5 mM, 65C

AJ606318

9Aii

[21,22]

X17469, X52126, U22376

 

F: AAATATAGTCAATGTCCCTCAGCC

R:ACAGGGGAACGCTTGGGAGT

1.5 mM, 62C

AJ606319

9B

     

F: ACAGAACCACACATGCAGCTACC

R:CACAATTTGGTTCCCTCCTC

  

9C

     

F: ACAGAACCACACATGCAGCTACC

R:TATTCCTTGGCAAAAACTGC

  

9D

     

F: ACAGAACCACACATGCAGCTACC

R:GGTCATTGCTGAAAAACTTGC

  

10A

 

U22376

    

F: ACAGAACCACACATGCAGCTACC

R:CATCCCTTGGCTTCTAATCATATAA

2.5 mM, 55C

AJ606322

11'

    

 

F: ACAGAACCACACATGCAGCTACC

R:CCTTTTGATAGCTGGGGTTACAGT

  

13A

 

U22376

    

F: AAACTTCTTCTGCTCACACCACTG

R:CTCACGCCTGTAATCCTAGCAC

1.5 mM, 60C

AJ606323

14'

    

 

F: AAACTTCTTCTGCTCACACCACTG

R:AAATACCAATGTTGGAATAGTAAT

  

14A

     

F: AAACTTCTTCTGCTCACACCACTG

R:TGGCTCAGGATTAATTTGGAA

2.5 mM, 50C

AJ606324

14B

     

F: AAACTTCTTCTGCTCACACCACTG

R:TGCAATATGTTCAATAATACCATGTG

  

14C

     

F: AAACTTCTTCTGCTCACACCACTG

R:TCTCGCTTATCCTGTAATGTGC

  
  1. The putative alternate splice variant is indicated in the 1st column, and the subsequent columns indicate lines of evidence that suggested the existence of this splice variant. The literature references and accession numbers for previously reported splice variants are provided. Ensembl transcripts were observed on the v.9.30a.1 (2/12/2002) Ensembl release. Gene predictions were suggested by Genscan, Fgenesh++ or Twinscan, and conserved regions were classified as intronic sequence of >70% homology over 100 bp with the syntenic mouse region. The RT-PCR primer sequences used to test the existence of each alternate exon are listed, followed by a column indicating whether this splice variant was detectable by RT-PCR, and the associated PCR conditions. The final column provides the accession number of our sequences for the confirmed alternate splice variant.
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BMC Genomics

ISSN: 1471-2164

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